Hi Matthew, can you please post your question in the GATK support forum?
That's where we're addressing Picard questions from now on.
http://gatkforums.broadinstitute.org/
When you post your question, please specify whether you are running on
regular WGS data or WGS data produced through a hybrid selection procedure
for enrichment.
Thanks!
On Fri, Apr 10, 2015 at 8:01 AM, <
samtools-help-requ...@lists.sourceforge.net> wrote:
> Send Samtools-help mailing list submissions to
> samtools-help@lists.sourceforge.net
>
> To subscribe or unsubscribe via the World Wide Web, visit
> https://lists.sourceforge.net/lists/listinfo/samtools-help
> or, via email, send a message with subject or body 'help' to
> samtools-help-requ...@lists.sourceforge.net
>
> You can reach the person managing the list at
> samtools-help-ow...@lists.sourceforge.net
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Samtools-help digest..."
>
>
> Today's Topics:
>
> 1. Trying to run CalculateHsMetrics over a whole genome
> (Wakeling, Matthew)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 10 Apr 2015 10:25:15 +0000
> From: "Wakeling, Matthew" <m.wakel...@exeter.ac.uk>
> Subject: [Samtools-help] Trying to run CalculateHsMetrics over a whole
> genome
> To: "samtools-help@lists.sourceforge.net"
> <samtools-help@lists.sourceforge.net>
> Message-ID:
> <
> amxpr03mb321c5a5bbb9997f89106408aa...@amxpr03mb321.eurprd03.prod.outlook.com
> >
>
> Content-Type: text/plain; charset="us-ascii"
>
> I recently tried to obtain coverage metrics for a whole genome sequencing
> project, using CalculateHsMetrics. Command line:
>
> java -Xmx30g -XX:ParallelGCThreads=4 -XX:ConcGCThreads=4 -jar picard.jar
> CalculateHsMetrics I=something.bam O=something.HS_metrics
> BAIT_INTERVALS=genome.interval_list TARGET_INTERVALS=genome.interval_list
> VALIDATION_STRINGENCY=SILENT METRIC_ACCUMULATION_LEVEL=SAMPLE
>
> This spends two hours calculating, and then fails in
> picard/analysis/directed/TargetMetricsCollector.java line 423:
>
> final short[] depths = new short[(int) this.metrics.TARGET_TERRITORY]; //
> may not use entire array
>
> Unfortunately in this case, this.metrics.TARGET_TERRITORY is the whole
> human genome, which is larger than Integer.MAX_INT, which rolls around to
> be a negative number, causing a java.lang.NegativeArraySizeException.
>
> Now, the limit on the size of a java array is fixed by the fact that
> arrays are indexed by an int, not a long. Possible fixes to this issue are
> splitting the depths array into multiple sub-arrays.
>
> Are there any plans to implement a fix to remove this limitation on
> CalculateHsMetrics?
>
> Thanks,
>
> Matthew
>
>
>
> ------------------------------
>
>
> ------------------------------------------------------------------------------
> BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT
> Develop your own process in accordance with the BPMN 2 standard
> Learn Process modeling best practices with Bonita BPM through live
> exercises
> http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual-
> event?utm_
> source=Sourceforge_BPM_Camp_5_6_15&utm_medium=email&utm_campaign=VA_SF
>
> ------------------------------
>
> _______________________________________________
> Samtools-help mailing list
> Samtools-help@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/samtools-help
>
>
> End of Samtools-help Digest, Vol 75, Issue 3
> ********************************************
>
--
Geraldine A. Van der Auwera, Ph.D.
Bioinformatics Scientist II
GATK Support & Outreach
Broad Institute
------------------------------------------------------------------------------
BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT
Develop your own process in accordance with the BPMN 2 standard
Learn Process modeling best practices with Bonita BPM through live exercises
http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- event?utm_
source=Sourceforge_BPM_Camp_5_6_15&utm_medium=email&utm_campaign=VA_SF
_______________________________________________
Samtools-help mailing list
Samtools-help@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/samtools-help
